Populate the Database

When Chewie-NS is deployed the Virtuoso database only contains the admin user, so we need to populate the database. Here we will describe the manual process to add a schema, loci and alleles to Chewie-NS. To add a schema with multiple loci and alleles please read Upload a schema to Chewie-NS.

To add data to the database we have to follow these steps:

Authenticate

First we need to authenticate the admin user and obtain a token that will allow a user to access the POST endpoints (GET endpoints don’t require authentication).

Add a new species

Afterwards, we need to access the species namespace on the Swagger page. There go to the /species/list POST endpoint and press the Try it out button.

Next fill the name field of the JSON payload with the name of the species to be added to the database and press the execute button.

{
    "name": "Yersinia pestis"
}

Output

{
    "message": "Yersinia pestis added to the NS."
}

Add a new for schema for a species

To add a new schema to a species we need to use the {species_id}/schemas POST endpoint and provide the species ID to add the new schema and also the following parameters, which are the parameters used to obtain the chewBBACA schema:

{
    "name": "string",
    "bsr": "string",
    "prodigal_training_file": "string",
    "translation_table": "string",
    "minimum_locus_length": "string",
    "size_threshold": "string",
    "chewBBACA_version": "string",
    "word_size": "string",
    "cluster_sim": "string",
    "representative_filter": "string",
    "intraCluster_filter": "string"
}

• name - schema name;

• bsr - blast score ratio;

• ptf - prodigal training file;

• translation_table - translation table;

• minimum_locus_length - minimum locus length;

• size_threshold - size threshold;

• chewBBACA_version - chewBBACA’s version;

• word_size - word size;

• cluster_sim - cluster_sim;

• representative_filter - representative_filter;

• intraCluster_filter - intraCluster_filter;

Add a new locus

We have a species and a schema now we need some loci. For that we need to go the loci namespace and add a new locus there.

There use the /list POST endpoint and fill the JSON payload with the locus prefix and the original name of the locus.

{
    "prefix": "string",
    "locus_ori_name": "string"
}

The output is the following:

{
    "message": "New locus added at http://127.0.0.1:5000/NS/api/loci/1 with the alias test-000001",
    "uri": "http://127.0.0.1:5000/NS/api/loci/1",
    "id": "1"
}

Add an allele to the locus

Now we need to add some alleles to the locus we added before. For that we need to go to the /loci/{loci_id}/alleles POST endpoint.

Just fill the following parameters and provide the locus ID obtained previously to give that locus a new allele.

{
    "sequence": "string",
    "species_name": "string",
    "uniprot_url": "string",
    "uniprot_label": "string",
    "uniprot_sname": "string",
    "sequence_uri": "string",
    "enforceCDS": false,
    "input": "manual, auto"
}

• sequence - DNA sequence of the allele;

• species_name - the name of the species we are tring to add the allele;

• uniprot_url - the url to the uniprot annotation;

• uniprot_label - the uniprot label;

• uniprot_sname - the uniprot submitted name;

• sequence_uri -

• enforceCDS - forces the endpoint to only accept CDS;

• input - the input type should be manual. The other options are for scripts that automate this process.

This is the output:

{
    "message": "A new allele has been added to http://127.0.0.1:5000/NS/api/loci/1/alleles/1"
}

Add locus to schema

Finally, we return to the species namespace, namely to the /{species_id}/schemas/{schema_id}/loci POST endpoint and we simply provide the locus ID to the JSON payload and we are done.

With these steps you sucessfully added a schema with one locus (with one allele) to the Nomenclature Server!